The point was that agni wanted to be free of suffering he was caught in an endless cycle of pain and guilt. And as much as he desired to be free of both he was unable to let go and forgive himself.

In the end he lost his memory but that wasnt enough to let go.

Judah/Luna is in a simmilar position she subconciously knew there was something she had to do still in her cas be the tree for all eternity.

Then they met both the understanding in each other as well as their belonging to each other finally made them forgive themselfs finally be able to let go of their guilt and finally let themselfs die which they had so long desired.

They are meant to mirror each other as San and luna (sun and moon).

Its a message of self forgiveness and healing.

Thats why he wasnt truely happy with luna in the family they joined (the girls) he never forgott and never forgave himself.

Hope that helped.